Genomic epidemiology of Streptococcus pyogenes across multiple centres in China

Streptococcus pyogenes causes a broad spectrum of invasive and non-invasive infections globally, associated with high morbidity and mortality. In mainland China, distribution of the emm genotype has shifted markedly over recent decades, with emm12 emerging as the dominant type. Meanwhile, resistance to macrolides, lincosamides, and tetracyclines has reached extremely high levels, severely limiting clinical treatment options and leading to the designation of S. pyogenes as a medium-priority pathogen by the World Health Organization.

A total of 133 non-duplicate S. pyogenes isolates were collected from seven hospitals in northern and southern China, covering five provinces and one municipality, between 2022 and 2024. All isolates underwent whole-genome sequencing, emm typing, multi-locus sequence typing, resistance gene detection, virulence gene analysis, and mobile genetic element identification.

All isolates were fully susceptible to penicillin, cefotaxime, levofloxacin, linezolid, vancomycin, and chloramphenicol. Resistance rates were 93.98% for erythromycin, 92.48% for clindamycin, and 81.95% for tetracycline, with erm(B) and tet(M) identified as the main resistance genes. emm12 (81.95%) and ST36 (81.20%) were the predominant types. The emm12-ST36 lineage was strongly associated with pharyngeal infections and acute suppurative tonsillitis. No M1_UK lineage was detected. Distinct virulence and mobile genetic element profiles were observed between emm12 and emm1 isolates.

S. pyogenes isolates analysed in this study showed extremely high resistance to macrolides, lincosamides, and tetracyclines. Penicillin remains the first-line therapy. For patients with penicillin allergy, alternative therapy should be guided by allergy severity, local susceptibility data, clinical guidelines, and antimicrobial susceptibility testing. The emm12-ST36 type was predominant among pharyngeal isolates and showed strong association with acute suppurative tonsillitis. Continuous genomic surveillance is critical for clinical treatment and infection control.